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Estimated time of infection vs. confirmed infections

Following the ideas from Tomas Pueyo's Medium post "Coronavirus: Why You Must Act Now" [1], we assume the average time from infection to death at 23 days [2]. The data is pulled from the COVID-19 Data Repository by Johns Hopkins CSSE [3] every hour. Countries with a minimnum of 1000 confirmed cases and 40 confirmed deaths are included in this analysis.

The time from infection to death is equal to the incubation period plus the time from symptoms to death. This is used to estimate the time of the infections that lead to the observed deaths. We take the last fatality rate per country (total_cases/total_deaths) to estimate the number of infections that are responsible for the observed deaths.

In the figures below, you can observe successive waves of infections (dashed), detections (black) and deaths (red) for each country. The upper panel shows the absolute number of events. The dashed lines show the estimated number of infections. The lower panel shows the normalized number of events. Here the temporal delay between the waves and the relative change between each other can be observed.

[1] https://medium.com/@tomaspueyo/coronavirus-act-today-or-people-will-die-f4d3d9cd99ca

[2] https://github.com/midas-network/COVID-19/tree/master/parameter_estimates/2019_novel_coronavirus

[3] https://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data/csse_covid_19_time_series

US
Brazil
India
Mexico
Russia
Peru
Indonesia
United Kingdom
Italy
Colombia
Iran
France
Argentina
Germany
South Africa
Spain
Poland
Ukraine
Turkey
Romania
Philippines
Chile
Ecuador
Hungary
Czechia
Malaysia
Canada
Pakistan
Bangladesh
Belgium
Tunisia
Bulgaria
Iraq
Vietnam
Thailand
Bolivia
Netherlands
Egypt
Burma
Japan
Portugal
Kazakhstan
Paraguay
Greece
Guatemala
Sweden
Morocco
Sri Lanka
Slovakia
Bosnia and Herzegovina
Austria
Nepal
Switzerland
Jordan
Honduras
Georgia
Serbia
Croatia
Saudi Arabia
Lebanon
Cuba
Israel
Moldova
Panama
Afghanistan
Azerbaijan
North Macedonia
Costa Rica
Armenia
Ethiopia
Uruguay
Lithuania
Algeria
Ireland
Kenya
Libya
Venezuela
Slovenia
Belarus
West Bank and Gaza
Zimbabwe
China
Dominican Republic
Oman
El Salvador
Zambia
Namibia
Latvia
Uganda
Sudan
Kosovo
South Korea
Albania
Nigeria
Cambodia
Denmark
Kyrgyzstan
Syria
Kuwait
Botswana
Malawi
Jamaica
Montenegro
United Arab Emirates
Mozambique
Senegal
Australia
Mongolia
Trinidad and Tobago
Cameroon
Angola
Estonia
Bahrain
Uzbekistan
Rwanda
Somalia
Eswatini
Finland
Ghana
Suriname
Congo (Kinshasa)
Madagascar
Guyana
Norway
Luxembourg
Taiwan*
Mauritania
Tanzania
Cote d'Ivoire
Haiti
Fiji
Lesotho
Bahamas
Qatar
Cyprus
Mali
Belize
Singapore
Malta
Papua New Guinea
Guinea
Cabo Verde
Congo (Brazzaville)
Saint Lucia
Gabon
Maldives
Togo
Burkina Faso
Hong Kong
Nicaragua
Mauritius
Djibouti
Barbados
Equatorial Guinea
Benin
South Sudan
Andorra
Tajikistan
Timor-Leste
Seychelles
Central African Republic

Ahead of the curve

Some countries start testing the population earlier in the outbreak than others. The time delay between the wave of deaths and the wave of confirmed cases is indicative for how early a country is detecting new cases ahead of the increase of deaths. Earlier detection means a better chances for successful isolation of an infected person and treatment of the desease.

We measure the distance of the maximum of cumulative deaths and new deaths to the number of infections to estimate the progression of the infection across countries.

If, in the early phase of the infection wave, the number of deaths rises faster than the number of confirmed cases, the distance drops, indicating that

A comparison of countries with respect to their mean time for reponse is presented below.

To determine the above values, we plot the number of confirmed cases (solid black lines) and the number of deaths (dashed black lines). From this, we measure the distance of the day of maximum deaths (dashed red lines) to the day of confirmed cases at this y-value.

The distance is indicative for how fast the humber of confirmed cases increases comapred to the increase of the number of deaths.

US
Brazil
India
Mexico
Russia
Peru
Indonesia
United Kingdom
Italy
Colombia
Iran
France
Argentina
Germany
South Africa
Spain
Poland
Ukraine
Turkey
Romania
Philippines
Chile
Ecuador
Hungary
Czechia
Malaysia
Canada
Pakistan
Bangladesh
Belgium
Tunisia
Bulgaria
Iraq
Vietnam
Thailand
Bolivia
Netherlands
Egypt
Burma
Japan
Portugal
Kazakhstan
Paraguay
Greece
Guatemala
Sweden
Morocco
Sri Lanka
Slovakia
Bosnia and Herzegovina
Austria
Nepal
Switzerland
Jordan
Honduras
Georgia
Serbia
Croatia
Saudi Arabia
Lebanon
Cuba
Israel
Moldova
Panama
Afghanistan
Azerbaijan
North Macedonia
Costa Rica
Armenia
Ethiopia
Uruguay
Lithuania
Algeria
Ireland
Kenya
Libya
Venezuela
Slovenia
Belarus
West Bank and Gaza
Zimbabwe
China
Dominican Republic
Oman
El Salvador
Zambia
Namibia
Latvia
Uganda
Sudan
Kosovo
South Korea
Albania
Nigeria
Cambodia
Denmark
Kyrgyzstan
Syria
Kuwait
Botswana
Malawi
Jamaica
Montenegro
United Arab Emirates
Mozambique
Senegal
Australia
Mongolia
Trinidad and Tobago
Cameroon
Angola
Estonia
Bahrain
Uzbekistan
Rwanda
Somalia
Eswatini
Finland
Ghana
Suriname
Congo (Kinshasa)
Madagascar
Guyana
Norway
Luxembourg
Taiwan*
Mauritania
Tanzania
Cote d'Ivoire
Haiti
Fiji
Lesotho
Bahamas
Qatar
Cyprus
Mali
Belize
Singapore
Malta
Papua New Guinea
Guinea
Cabo Verde
Congo (Brazzaville)
Saint Lucia
Gabon
Maldives
Togo
Burkina Faso
Hong Kong
Nicaragua
Mauritius
Djibouti
Barbados
Equatorial Guinea
Benin
South Sudan
Andorra
Tajikistan
Timor-Leste
Seychelles
Central African Republic